[Bioperl-l] call for help and comments on module

Dan Kortschak dan.kortschak at adelaide.edu.au
Tue Dec 22 00:51:30 EST 2009

Hi Mark,

maptool either outputs to stdout or a specified file - I chose to use a
specified file and run it that way, but I've tried the redirect a you
suggest, with the same failure result. I think it's a strangeness of
maptool (which may well be a reason for it being dropped - also note the
maptool output doesn't seem reasonable for the test data provided even
when run from the command line).

It's probably a result of difficult interaction between IPC::Run and
maptool. Any funkiness in your code is not likely to be a cause as I've
deeply analysed what is being passed to IPC::Run, and I've quite
extensively modified the IPC run handling method from your code to take
into account the differences between a single executable with many
commands as the base code managed from a cluster of executables each
taking a small subset of different filespecs as bowtie needs. My
funkiness will undoubtedly swamp yours.

Resolution: Will drop bowtie-maptool from module.

(Should test maqconvert - if it fails, this will be dropped also unless
someone asks otherwise).

When the module copes with 0.11.* properly I'll start thinking about
0.12.* which has colourspace handling to deal with.


On Tue, 2009-12-22 at 00:19 -0500, Mark A. Jensen wrote:
> Hey Dan, 
> It looks like if the outfile isn't specified on the commandline for
> maptool, then the align is written to stdout. So, you could 
> try this workaround in in Bowtie/Config.pm:
> our %command_files = (
>     'single'     => [qw( ind seq #out )],
>     'paired'     => [qw( ind seq seq2 #out )],
>     'crossbow'   => [qw( ind seq #out )],
>     'build'      => [qw( ref out )],
>     'inspect'    => [qw( ind >#out )],
>     'convert'    => [qw( bwt out bfa )],
> -    'map'        => [qw( bwt #out )]
> +    'map'        => [qw( bwt >#out )]
>     );
> which should be transparent to the user. If this works, then
> there is probably something funky going on with IPC::Run
> + maptool; if it doesn't, then the funkiness is prob. in my code.
> I notice, however, that both bowtie-maptool and bowtie-maqconvert
> have been removed from the 0.12.0-beta release 
> (http://bowtie-bio.sourceforge.net/index.shtml)...
> cheers MAJ

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